A fast and accurate SNP detection algorithm for next-generation sequencing data
A fast and accurate SNP detection algorithm for next-generation sequencing data
复制标题
用于下一代测序数据的快速准确的 SNP 检测算法
DOI：
10.1038/ncomms2256
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发表时间：
2012-12-01
影响因子：
16.6
通讯作者：
Wang, Junwen
中科院分区：
文献类型：
--
作者：
Xu, Feng;Wang, Weixin;Wang, Junwen
已经开发了各种方法用于从下一代测序数据中调用单核苷酸多态性。然而，为了获得令人满意的性能，这些方法中的大多数需要昂贵的高深度测序。在这里，我们提出了一个快速，准确的单核苷酸多态性检测程序，使用二项分布为基础的算法和突变概率。我们广泛评估了来自癌症基因组图谱项目的正常和癌症下一代测序数据以及来自1,000个基因组项目的汇总数据。我们还比较了几个国家的最先进的单核苷酸多态性调用程序的性能，并评估其利弊。我们证明，我们的程序是一种快速，高度准确的单核苷酸多态性检测方法，特别是当序列深度低。该程序可以在标准台式计算机上在4小时内完成10倍人类基因组下一代测序数据（30千兆字节）的单核苷酸多态性调用。
Various methods have been developed for calling single-nucleotide polymorphisms from next-generation sequencing data. However, for satisfactory performance, most of these methods require expensive high-depth sequencing. Here, we propose a fast and accurate single-nucleotide polymorphism detection program that uses a binomial distribution-based algorithm and a mutation probability. We extensively assess this program on normal and cancer next-generation sequencing data from The Cancer Genome Atlas project and pooled data from the 1,000 Genomes Project. We also compare the performance of several state-of-the-art programs for single-nucleotide polymorphism calling and evaluate their pros and cons. We demonstrate that our program is a fast and highly accurate single-nucleotide polymorphism detection method, particularly when the sequence depth is low. The program can finish single-nucleotide polymorphism calling within four hours for 10-fold human genome next-generation sequencing data (30 gigabases) on a standard desktop computer.